jgi_mt_header_v16.json

{
    "Seq Project ID (No edit)": {
        "1": "Prefilled",
        "2": "1191234",
        "sub_port_mapping": "jgi_seq_project"
    },
    "Seq Project Name (No edit)": {
        "1": "Prefilled",
        "2": "JGI Pond metatranscriptome",
        "sub_port_mapping": "jgi_seq_project_name"
    },
    "Sample ID (No edit)": {
        "1": "Prefilled",
        "2": "187654",
        "sub_port_mapping": "jgi_samp_id"
    },
    "Source Sample GUID": {
        "1": "List the sample's Globally Unique Identifier, if available. More details are available on the \"instructions\" tab.",
        "2": "igsn:IEBWE008U",
        "sub_port_mapping": "source_mat_id"
    },
    "Sample Name*": {
        "1": "Give the sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain ASCII characters only.",
        "2": "JGI_pond_041618",
        "sub_port_mapping": "jgi_sample_name"
    },
    "Biological replicate/sample group Name* (required for RNA expression and Stable Isotope Probing (SIP) source samples)": {
        "1": "Samples that are biological replicates should have the same group name.  If your project does not contain biological replicates, give each sample its own group name.",
        "2": "West",
        "sub_port_mapping": "replicate_group"
    },
    "Isotope Label* (required for Stable Isotope Probing (SIP source samples)": {
        "1": "Choose from the following: C13, N15, O18, Unlabeled ",
        "2": "",
        "sub_port_mapping": "isotope_exposure"
    },
    "Isotopolog / PubChem CID* (required for Stable Isotope Probing (SIP source samples)": {
        "1": "Value must be an integer >=0.",
        "2": ""
    },
    "Concentration* (ng/ul)": {
        "1": "Must be calculated using a fluorometric method; value >0 and <2000.",
        "2": "100",
        "sub_port_mapping": "nuc_acid_concentration"
    },
    "Volume* (ul)": {
        "1": "Value must be >0 and <1000 (values <25 by special permission only).",
        "2": "25",
        "sub_port_mapping": "jgi_sample_volume"
    },
    "Absorbance 260/280* (required for metagenome improved drafts or any PacBio libraries)": {
        "1": "Recommended value is between 1 and 3.",
        "2": "",
        "sub_port_mapping": "nuc_acid_absorb1"
    },
    "Absorbance 260/230* (required for metagenome improved drafts or any PacBio libraries)": {
        "1": "Recommended value is between 1 and 3.",
        "2": "",
        "sub_port_mapping": "nuc_acid_absorb2"
    },
    "Tube or Plate Label*": {
        "1": "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label.",
        "2": "Pond_MT_041618",
        "sub_port_mapping": "container_name"
    },
    "Sample Container*": {
        "1": "tube or plate (96-well)",
        "2": "plate",
        "sub_port_mapping": "cont_type"
    },
    "Plate location (well #)* required if samples provided in a plate.": {
        "1": "Corner wells must be blank. For partial plates, fill by columns. Leave blank if the sample will be shipped in a tube.",
        "2": "B2",
        "sub_port_mapping": "cont_well"
    },
    "Sample Format*": {
        "1": "Choose from the following: Pellet, Ethanol, MDA Reaction Buffer, PBS, TE, Water, Low EDTA TE, 10 mM Tris-HCl, Gentegra-DNA, Gentegra-RNA",
        "2": "Water",
        "sub_port_mapping": "jgi_sample_format"
    },
    "Was Sample DNAse treated?*": {
        "1": "Y/N.  Note DNAse treatment is required for all RNA samples.",
        "2": "Y",
        "sub_port_mapping": "dnase"
    },
    "Known / Suspected Organisms": {
        "1": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.",
        "2": "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)"
    },
    "Biosafety Material Category*": {
        "1": "Metagenome (Environmental) or Metagenome (Host-associated)",
        "2": "Metagenome (Environmental)",
        "sub_port_mapping": "biosafety_mat_cat"
    },
    "Sample Isolation Method*": {
        "1": "Describe the method/protocol/kit used to extract DNA/RNA.",
        "2": "phenol/chloroform extraction",
        "sub_port_mapping": "rna_isolate_meth"
    },
    "Collection Year*": {
        "1": "Year in which the sample was collected. More details on the \"instructions\" tab.",
        "2": "2018",
        "sub_port_mapping": "collection_year"
    },
    "Collection Month*": {
        "1": "Month in which the sample was collected. Use the full name of the month. More details on the \"instructions\" tab.",
        "2": "April",
        "sub_port_mapping": "collection_month_name"
    },
    "Collection Day*": {
        "1": "Day on which the sample was collected. More details on the \"instructions\" tab.",
        "2": "1",
        "sub_port_mapping": "collection_day"
    },
    "Sample Isolated From*": {
        "1": "Describe where the sample originated.",
        "2": "Freshwater pond",
        "sub_port_mapping": "sample_isolated_from"
    },
    "Collection Site or Growth Conditions* (required for RNA samples)": {
        "1": "Provide information on the specific tissue type or growth conditions.",
        "2": "untreated pond water",
        "sub_port_mapping": "env_medium"
    },
    "Latitude*": {
        "1": "Latitude of sample collection. Value must be numeric only and between -90 and 90.",
        "2": "37.910076",
        "sub_port_mapping": "latitude"
    },
    "Longitude*": {
        "1": "Longitude of sample collection. Value must be numeric only and between -180 and 180.",
        "2": "-122.065186",
        "sub_port_mapping": "longitude"
    },
    "Depth* (in meters) or minimum depth if a range": {
        "1": "Depth below the surface. If the sample was collected from a range of depths, indicate the shallowest depth. Value must be numeric and 0 or greater.",
        "2": "0.5",
        "sub_port_mapping": "minimum_depth"
    },
    "Maximum depth (in meters) if a range": {
        "1": "If the sample was collected from a range of depths, indicate the maximum depth below the surface. Value must be numeric and >0.",
        "2": "",
        "sub_port_mapping": "maximum_depth"
    },
    "Elevation* (in meters) or minimum elevation if a range": {
        "1": "Elevation (from sea level) of sample collection. If the sample was collected from a range of elevations, indicate the elevation nearest to sea level.Value must be numeric and can be either positive or negative.",
        "2": "39.9",
        "sub_port_mapping": "elev"
    },
    "Maximum elevation (in meters) if a range": {
        "1": "If the sample was collected from a range of elevations, indicate the elevation farthest from sea level. Value must be numeric and can be either positive or negative.",
        "2": ""
    },
    "Country*": {
        "1": "Country or ocean where the sample was collected.",
        "2": "USA",
        "sub_port_mapping": "country_name"
    },
    "Sample Contact Name": {
        "1": "Prefilled",
        "2": "John Jones",
        "sub_port_mapping": "jgi_sample_contact"
    },
    "Seq Project PI Name (No edit)": {
        "1": "Prefilled",
        "2": "Jane Johnson",
        "sub_port_mapping": "jgi_project_pi"

    },
    "Tissue Contact Name": {
        "1": "Prefilled",
        "2": "Jordan James"
    },
    "Proposal ID (No edit)": {
        "1": "Prefilled",
        "2": "504000",
        "sub_port_mapping": "jgi_proposal_id"
    }
}